4BHM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF MOSUB1-DNA COMPLEX REVEALS A NOVEL DNA BINDING MODE

Authors :   J. Huang, H. Liu, Y. Zhao, D. Huang, J. Liu, Y. Peng

Date :   04 Apr 13 (Deposition) - 23 Apr 14 (Release) - 18 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H,I

Keywords :   Transcription-Dna Complex, Ssdna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Huang, Y. Zhao, H. Liu, D. Huang, X. Cheng, W. Zhao, I. A. Taylor, J. Liu, Y. L. Peng
Substitution Of Tryptophan 89 With Tyrosine Switches The Dna Binding Mode Of Pc4.
Sci. Rep. V. 5 8789 2015
PubMed-ID: 25739870 | Reference-DOI: 10.1038/SREP08789

Molecule 1 - MOSUB1 TRANSCRIPTION COFACTOR
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 42-120
	Organism Scientific	:	MAGNAPORTHE ORYZAE
	Organism Taxid	:	318829

*Molecule 2 - 5'-D(TPTPTPTPTPTPTPTP)-3'*
	Chains	:	G, H, I
	Organism Scientific	:	MAGNAPORTHE ORYZAE
	Organism Taxid	:	318829
	Synonym	:	SSDNA
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY C:112 , HIS C:113 , ASP C:114	BINDING SITE FOR RESIDUE SO4 C1117
2	AC2	SOFTWARE	ASP D:42 , ALA D:43 , ARG D:56	BINDING SITE FOR RESIDUE SO4 D1117
3	AC3	SOFTWARE	LYS C:54 , HOH C:2021	BINDING SITE FOR RESIDUE SO4 E1117
4	AC4	SOFTWARE	ASN F:105 , ARG F:109	BINDING SITE FOR RESIDUE SO4 F1117
5	AC5	SOFTWARE	HIS A:113 , HOH A:2017	BINDING SITE FOR RESIDUE SO4 A1117

(no "SS Bond" information available for 4BHM)

(no "Cis Peptide Bond" information available for 4BHM)

(no "SAP(SNP)/Variant" information available for 4BHM)

(no "PROSITE Motif" information available for 4BHM)

(no "Exon" information available for 4BHM)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:79
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:79
                                    51        61        71        81        91       101       111         
         G4NEJ8_MAGO7    42 GSQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee....eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4bhm A  38 GSQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    47        57        67        77        87        97       107

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:78
                                    52        62        72        82        92       102       112        
         G4NEJ8_MAGO7    43 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee....eeeeeeee..eeeeeeeeeee..-.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4bhm B  39 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAG-EMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    48        58        68        |-|       88        98       108        
                                                                 77 |                                     
                                                                   79

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:79
                                    51        61        71        81        91       101       111         
         G4NEJ8_MAGO7    42 GSQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeee....eeeeeeee..eeeeeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4bhm C  38 GSQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    47        57        67        77        87        97       107

Chain D from PDB  Type:PROTEIN  Length:75
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:78
                                    52        62        72        82        92       102       112        
         G4NEJ8_MAGO7    43 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee....eeeeeeee..eeeeeeeeee..---.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4bhm D  39 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEA---MKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    48        58        68       | - |      88        98       108        
                                                                76  80

Chain E from PDB  Type:PROTEIN  Length:75
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:77
                                    53        63        73        83        93       103       113       
         G4NEJ8_MAGO7    44 QVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee....eeeeeeee..eeeeeeeeee..--..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4bhm E  40 QVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEA--EMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    49        59        69      | 79        89        99       109       
                                                               76 79

Chain F from PDB  Type:PROTEIN  Length:78
 aligned with G4NEJ8_MAGO7 | G4NEJ8 from UniProtKB/TrEMBL  Length:162

    Alignment length:78
                                    52        62        72        82        92       102       112        
         G4NEJ8_MAGO7    43 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 120
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee....eeeeeeee..eeeeeeeeee......eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4bhm F  39 SQVDAEGNPFWEISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAELRSRGHDIT 116
                                    48        58        68        78        88        98       108

Chain G from PDB  Type:DNA  Length:8
                                        
                 4bhm G   1 TTTTTTTT   8

Chain H from PDB  Type:DNA  Length:8
                                        
                 4bhm H   1 TTTTTTTT   8

Chain I from PDB  Type:DNA  Length:7
                                       
                 4bhm I   1 TTTTTTT   7

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4BHM)

(no "CATH Domain" information available for 4BHM)

(no "Pfam Domain" information available for 4BHM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (G4NEJ8_MAGO7 | G4NEJ8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bhm)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4bhm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	G4NEJ8_MAGO7 \| G4NEJ8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	G4NEJ8_MAGO7 \| G4NEJ8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	G4NEJ8_MAGO7 \| G4NEJ8	:	4agh

(no "Related Entries Specified in the PDB File" available for 4BHM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File